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Bulked segregant analysis with whole-genome resequencing to map QTL involved in Phytophthora crown and root rot resistance in Cucurbita pepo

Gregory Vogel: Plant Breeding and Genetics Section, Cornell University

<div>Phytophthora crown and root rot, caused by the broad-host range oomycete pathogen <em>Phytophthora capsici</em>, causes severe yield loss in squash and pumpkin (<em>Cucurbita pepo </em>ssp.<em> pepo</em>) in many areas. No source of complete resistance to <em>P. capsici</em> has been identified in <em>C. pepo, </em>but breeding lines with partial disease resistance were developed at Cornell University, using gray zucchini landrace PI 615089 as a source of resistance. These breeding lines display reduced crown and root rot symptoms when inoculated with several <em>P. capsici</em> isolates. The goal of this project is to identify quantitative trait loci (QTL) controlling partial resistance in these lines, potentially a complex genetic architecture. In that light, we employed a bulk-segregant analysis using large populations and deep sequencing of DNA from bulks, providing sufficient statistical power to detect small-effect QTL. Over 13,000 F<sub>2</sub> individuals from a biparental population segregating for partial root and crown rot resistance were evaluated in a greenhouse disease screen of seedlings. The most susceptible and resistant individuals were identified and bulked separately, with each bulk constituting approximately 15% of the total population. Whole-genome resequencing of pooled DNA from bulks will be performed to map QTL by identifying linked variants having significant differences in allele frequencies between the bulks.</div>